Can regime shifts in reproduction be explained by changing climate and food availability? ...

• Main Authors: Tirronen, Maria, Depestele, Jochen, Kuparinen, Anna
• Format: Software
• Language: unknown
• Published: Zenodo 2023
• Subjects: stock-recuitment; Environmental forcing; Change-point detection; Bayesian; Regime shifts; depensation; Allee effect; Atlantic cod; Irish Sea; atlantic cod
• Online Access: https://dx.doi.org/10.5281/zenodo.7257171; https://zenodo.org/record/7257171

Marine populations often show considerable variation in their productivity, including regime shifts. Of special interest are prolonged shifts to low recruitment and low abundance which occur in many fish populations despite reductions in fishing pressure. One of the possible causes for the lack of recovery has been suggested to be the Allee effect (depensation). Nonetheless, both regime shifts and the Allee effect are empirically emerging patterns but provide no explanation about the underlying mechanisms. Environmental forcing, on the other hand, is known to induce population fluctuations and has also been suggested as one of the primary challenges for recovery. Yet, traditional stock-recruitment models used in fisheries management have been time-invariant and considered only density-dependence. In the present study, we build upon recently developed Bayesian change-point models to explore the contribution of food and climate as external drivers in recruitment regime shifts, while accounting for ... : The file environmental_predictors.Rmd describes data pre-processing. The folder BOCPD provides scripts for fitting the change point models to the empirical data. Consider parallel computing for efficiency. The empirical data are not adjusted, consider lags, when needed (see the article and its supplementary material). The results data enable model comparison based on the negative log marginal likelihood (nlml).Funding provided by: Academy of Finland Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002341 Award Number: 317495Funding provided by: European Research Council Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100000781 Award Number: COMPLEX-FISH 770884Funding provided by: H2020 Societal Challenges Crossref Funder Registry ID: http://dx.doi.org/10.13039/100010676 Award Number: 101000318 ...